Could someone please tell me how to unsubscribe from this list? I couldn't find it on the website. Thanks On Jul 2, 2015 4:56 AM, "Milde, Christopher" < christopher.mi...@zi-mannheim.de> wrote:
> Dear Freesurfers, > > I have problems converting .nii.gz files into .mgh files needed e.g. for > performing ROI analysis. > > I used mri_vol2surf and mri_vol2vol to produce .mgh files either to > visualize contrast estimates and significance maps on volumes or surfaces > > I think the problem is due to voxel resolution mismatches between source > and registration files but I don't know how to solve this problem. > > I worked with different registration files: the register.dof6.dat > (originally outpu from the preproc-sess) as well as register.dat and > register.lta by running bbregister for the template.nii.gz > > > > --------------------------------------------------------------------------------------------------------------------------- > here is an example command: > > # resample to surface > > mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg > $sub/bold/register.lta --projfrac 0.5 \ > --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh > > > mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg > $sub/bold/register.lta --projfrac 0.5 \ > > --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh > srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz > srcreg = PM_04001/bold/register.lta > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > Done loading volume > regio_read_register: loading lta > reading extra input line subject PM_04001 > reading extra input line fscale 0.150000 > WARNING: the voxel resolution in the source volume (1,1,1) differs > from that listed in the registration file (2.29167,2.29167,2.99) > Reading surface /home/christopher/subjects/PM_04001/surf/lh.white > Done reading source surface > Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Number of source voxels hit = 5 > Writing to PM_04001/bold/lh.sig.mgh > Dim: 126553 1 1 > > > ---------------------------------------------------------------------------------------------------------------------------- > > Thanks, > > Christopher > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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